An efficient index for the colored, compacted, de Bruijn graph
☆112Mar 11, 2026Updated 2 months ago
Alternatives and similar repositories for pufferfish
Users that are interested in pufferfish are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 5 months ago
- Squeakr: An Exact and Approximate k -mer Counting System☆86Feb 23, 2025Updated last year
- semi-reference-based short read compression☆11Mar 5, 2019Updated 7 years ago
- Histosketching Using Little Kmers☆57May 25, 2023Updated 2 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Jun 4, 2022Updated 3 years ago
- Minhash Index Extended to Knead Kmer Intersection☆11Mar 18, 2020Updated 6 years ago
- ☆20Aug 18, 2020Updated 5 years ago
- Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index☆86Mar 7, 2024Updated 2 years ago
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆40Jul 15, 2019Updated 6 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆54May 9, 2026Updated last week
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- compacted de Bruijn graph construction in low memory☆101Nov 4, 2025Updated 6 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆24Apr 2, 2021Updated 5 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Feb 26, 2026Updated 2 months ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated last year
- REINDEER REad Index for abuNDancE quERy☆56Jul 6, 2025Updated 10 months ago
- The Modular Aligner and The Modular SV Caller☆47Jul 18, 2023Updated 2 years ago
- A tool for projecting genomic alignments to transcriptomic coordinates☆37May 28, 2024Updated last year
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- Fast and accurate genomic distances using HyperLogLog☆162Jan 19, 2023Updated 3 years ago
- The Dagstuhl Format for Assembly☆13Oct 16, 2017Updated 8 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆198Mar 8, 2022Updated 4 years ago
- ☆12Sep 7, 2019Updated 6 years ago
- ntHash implementation in Rust☆36Jul 12, 2024Updated last year
- Reference-free variant discovery in large eukaryotic genomes☆42Jul 13, 2021Updated 4 years ago
- Bonsai: Fast, flexible taxonomic analysis and classification☆70Apr 9, 2024Updated 2 years ago
- Filter of Pairwise Alignement☆44Jan 31, 2022Updated 4 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Estimating k-mer coverage histogram of genomics data☆78Mar 13, 2026Updated 2 months ago
- A succinct colored dBG representation☆12Sep 11, 2018Updated 7 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆286Dec 29, 2025Updated 4 months ago
- CAMITAX: Taxon labels for microbial genomes☆31Dec 14, 2023Updated 2 years ago
- a wee tool for random access into BGZF files.☆86May 10, 2018Updated 8 years ago
- A fast K-mer counter for high-fidelity shotgun datasets☆144Jan 19, 2026Updated 4 months ago
- De novo genome assembler.☆12Jul 30, 2018Updated 7 years ago
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Dec 16, 2019Updated 6 years ago
- ☆21Dec 26, 2025Updated 4 months ago